I saw a relevant post on the Blizzard forums, commenting that once something is in your currency pane you can never get rid of it, and because of this permanence the developers are careful about adding new currencies. Annoying as it is to spend an inventory slot on a commendation for a faction, you can at least discard them next patch or whenever you are done with them.

I kept more than 90 lesser charms because I knew once I had hit exalted with all the existing reps I'd stop doing dailies. At this point I do a single tillers daily for the ironpaw token, work my farm, and maybe do the archaeology daily (mostly for the crate to turn in for fragments). Now with a supply of them I can work on other toons or other games without having to farm up 90 of them each week.